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Comparison of measures of marker informativeness for ancestry and admixture mapping

Authors :
Ding Lili
Wiener Howard
Abebe Tilahun
Altaye Mekbib
Go Rodney CP
Kercsmar Carolyn
Grabowski Greg
Martin Lisa J
Khurana Hershey Gurjit K
Chakorborty Ranajit
Baye Tesfaye M
Source :
BMC Genomics, Vol 12, Iss 1, p 622 (2011)
Publication Year :
2011
Publisher :
BMC, 2011.

Abstract

Abstract Background Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases and simulated data have been interrogated in admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (FST), Informativeness for Assignment Measure (In), and the Absolute Allele Frequency Differences (delta, δ). The objectives are to compare these measures of informativeness to select SNP markers for ancestry inference, and to determine the accuracy of AIM panels selected by each measure in estimating the contributions of the ancestors to the admixed population. Results FST and In had the highest Spearman correlation and the best agreement as measured by Kappa statistics based on deciles. Although the different measures of marker informativeness performed comparably well, analyses based on the top 1 to 10% ranked informative markers of simulated data showed that In was better in estimating ancestry for an admixed population. Conclusions Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.

Details

Language :
English
ISSN :
14712164 and 17318106
Volume :
12
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
edsdoj.173181069cc2453e9e92b49e9c6abb98
Document Type :
article
Full Text :
https://doi.org/10.1186/1471-2164-12-622